Tuesday, January 25, 2011

Sciences are always in a state of ebb and flow (sorry), and topics of study fall in or out of fashion in response to paradigms shifts, methodological advances, and to support necessary ecological applications. For the sake of curiosity, I've compiled the top keywords from ecology publications in 2010. Obviously there are many covariates, but it should come as no surprise that the top words were "biodiversity" (667 times), "climate change" (293), and "conservation" (274); other popular keywords were "evolution" (277), "population (ecology)" (273), and the rather vague "patterns" (196).(click image for larger view)

Thursday, January 20, 2011

Twenty years of research has repeatedly shown that communities with greater diversity result higher functioning -namely greater production of biomass. One of the major mechanisms producing this relationship is that different species use differing resources, such that their complementary use of resources uses the total resource pool more thoroughly, thus converting more resources into biomass. Resource preference is the product of evolution and how organisms have adapted to using various resources can influence the strength of the diversity-function.

In a recent paper in Nature, Dominique Gravel and colleagues test how the evolution of specialization versus general resource use affect the strength of the diversity-function relationship. They use bacteria strains that have undergone evolution on diverse resources (generalist) versus on a singular resource (specialist). The resources in their case are different carbon substrates.

Assemblages of generalists were able to use many available resources and generally had greater productivity than specialist assemblages. Generalists also show an increasing relationship between diversity and productivity, because no generalist used all resources and they still showed some preferences. Combining multiple such generalists meant that more of the total resource pool was consumed. Specialists also resulted in the positive relationship, but a much steeper one. Because specialist use many fewer carbon substrates, additional specialists meant that new resources were tapped into. Thus increasing specialist diversity resulted in more new resources being consumed than with the generalist species.

While these results are logical, they are important for two reasons. First is that the strength of the relationship between diversity and function is mechanistically determined by the resource use efficiency of individual strains, and how many of the total substrates they can use. The mechanisms producing different relationships in previous experiments were hypothesized after the results analyzed, as opposed to being predicted. Second, recent work has shown that evolutionary history seems to be a better explanation of community function than the number of species. These results show how the history of evolution can have important consequences for function.

Tuesday, January 11, 2011

In discussions of the larger societal implications of scientific findings, the question of who is a scientist is frequently asked. I've talked with with creationists who invoke the authority of someone who has a PhD in a scientific discipline and happens to share their belief of supernatural origins, as a scientific authority. Does the fact that I have a PhD in ecology and evolutionary biology make me scientist or is being scientist something more?

This is an important question. It goes to the core of whose authority we believe for public discussion of such issues as climate change, evolution, risks of vaccines, and so on. Regardless of how we define 'scientist', a scientist participates in science by publishing peer-reviewed research articles in scientific publications. This notion of who is a scientist has been enjoyably stretched by the publication of a paper in Biology Letters by a group of elementary school children from Blackawton, UK. In consultation with a academic scientist and under the supervision of teachers, 25 8-10 year olds devised and carried out an experiment on bee visual perception and behavior, and wrote up their results into a publishable manuscript.

The students trained bees by offering them nectar rewards in different color containers. They then allowed these trained bees to forage in multicolored arenas and they conclusively show that the bees unambiguously select the colored containers they were trained on. Bess learn and adapt their behavior based on previous experience.

Publishing a paper by a group of children may sound like a gimmick, but the study is very interesting. The commentary from the journal says it best: "The children's findings show that bees are able to alter their foraging behaviour based on previously learned colours and pattern cues in a complex scene consisting of a (local) pattern within a larger (global) pattern . As there has been little testing of bees learning colour patterns at small and large scales, the results can add considerably to our understanding of insect behaviour."

The paper is extremely enjoyable to read and will have you chuckling to yourself. Sincerity pours from the words and I was left wondering if I could have reasoned so well at that age. The children develop hypotheses using information available to them, such as watching Dave Letterman's 'Stupid Dog Tricks'. Reading this article made me realize why I love being scientist. The students note that "This experiment is important, because, as far as we know, no one in history (including adults) has done this experiment before" and because they were given the opportunity to carryout this study they "also discovered that science is cool and fun because you get to do stuff that no one has ever done before". Too true. I could not have said it better myself.

Being scientist can mean a lot of things, it can mean knowledge (which the Latin origin, Scientia means), it can mean training and acquired skills, but at its core, being a scientist means conducting research, testing hypotheses and writing publications that are deemed acceptable by other scientists. Therefore the children of Blackawton are scientists, I am a scientist.

Tuesday, January 4, 2011

The Internet is not just for lolcats and porn anymore, scientists have begun using it in constructive ways. The past few weeks’ controversy about the ability (or lack thereof) of bacteria to incorporate arsenic exemplifies how the relationship between science and the Internet is changing. If you’ve missed the debate over the recent Science paper, researchers funded by NASA’s exobiology/evolutionary biology program published experimental results suggesting that a Halomonas speciescould incorporate arsenic into its DNA in the absence of available phosphorus. This paper received extensive attention in the mainstream media, but also vocal criticism, which was expressed primarily through postings and comments on scientific blogs. Until recently, for scientific communication the Internet has functioned primarily as an electronic source of published journal articles. Earlier attempts to take advantage of the Internet’s potential (immediacy, accessibility, and ability to connect individuals, organizations, and ideas) in scientific discourse have been mixed (e.g. Nature Precedings versus PLoS ONE). The use of blogs as a forum for scientific debate suggests that this is changing: posters tended to be active scientists and the comments were similarly knowledgeable. In contrast to this online approach, the authors of the Science paper stated that they would only respond to peer-reviewed critiques and would not engage in discussions on the blogosphere.

The story of the arsenic-utilizing bacteria highlights an emergent tension in the transition to internet-based scientific discourse. Traditional communication in science has been primarily unidirectional, from the authors of a study to the readership of a journal. Any discourse transpired on the pages of a journal, regulated by editorial and peer review. This gatekeeping meant that this discourse was technically sound and kept personal grudges and tangential discussions to a minimum. This also meant, however, that only a few voices were heard, the discussion was slow (occurring over months) and only happened for one back and forth (journals will not devote precious page space to on-going discussions and debates).

This method of discourse is changing. Journals have experimented with online discussion or commenting features on their websites. Methods in Ecology and Evolution, for example, has a correspondence page with discussion threads for each paper they publish, and PloS ONE allows for comments to be posted to every paper they publish. While, in concept, these are positive developments for scientific communication, commenting features are seldom, if ever, used. The main obstacle to their success is that they are only available on the publishers’ websites, but scientists access articles in many different ways, from database searches to library links. Few scientists actually go to individual journal websites to access papers. This is not to say that there are not discussions about scientific papers occurring online. As highlighted by the arsenic bacterial episode, blogs are an important avenue for discussing and disseminating new ideas in science. Blogs may not, however, actually foster conversations very well. One person or a few people usually run them and there is little discussion among blogs (a comment on a blog post at blog X will not be part of the discussion of the same story at blog Y). Rather, the greatest potential to foster discourse is through virtual networks where people are linked together either through friendships or professional self-identification (e.g., as fisheries biologists), with Google Reader being a particularly powerful communication tool.

It’s exciting to think about what the future of science will look like, given the changes that we’ve already started to see.The major upside of new channels of communication is that they give us the potential to quickly reach thousands of readers, instead of the handful that usually read any given journal article.They also let us communicate in both directions, and in real time.The pitfall, of course, is that they’re free-for-alls; anyone can blog about science.

But here’s what’s unexpected: these free-for-alls have been amazingly reliable at filtering out the bad and promoting the good.Inaccuracies are pulled from Wikipedia faster than anyone had predicted, the social news site Reddit is “astonishingly” altruistic, with users eliminating offensive or erroneous comments from the site and promoting other users’ questions and problems, and the reputations of blogs are shattered if their content becomes unreliable. Social networking has revolutionized the way we consume news, with sites like Facebook and Twitter launching the best articles into viral webspace. The open-access world has evolved self-regulating mechanisms that work surprisingly well so far and if these media are to continue to grow, we will have to ensure that these mechanisms remain built-in.

Seems like an easy task, right?Apparently not. For some reason, academics are slow and conservative when it comes to adopting new media.A letter to Nature two weeks ago scolded scientists for not contributing their share to Wikipedia pages.Various facebooks for academics, like Mendeley and ResearchGATE have emerged, but last week, another Nature article complained that researchers aren’t jumping on the bandwagon.These sites are potential collaborative goldmines, but we seem to be incapable mastering what tweens can do with two thumbs.

It’s not so hard to imagine a world where anyone with a broadband connection can contribute creative ideas to science, the good ideas get automatically filtered to the top and the information is all free to anyone.In this world, children count ants (or bees!) in their backyards and upload their data to global networks.Revolutionary discoveries are published instantly on blogs and thousands of scientists get to decide if they’re valid.Every gene ever sequenced and every tree height ever measured can be readily downloaded in an Excel (or OpenOffice) spreadsheet.In this world, the report on our little arsenophilic friends might never have been published in Science, because instead of being reviewed by two referees, the thousands of readers on the blogosphere would have filtered it out, if was in fact porous.

Academics should be the first, not the last, to adopt new communication tools.We are no longer limited by the postal service, email or PDFs; the web has gone 2.0 and we should follow suit.So go forth, young researchers, and blog, edit and share.And then go tweet about it all so your eight year-old kid knows how hip you are.